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[[Image:LifetrackingCover1.jpg|right|318x450px|LifetrackingCover1.jpg]] Open Science and its Discontents  
[[Image:LifetrackingCover1.jpg|right|318x450px|LifetrackingCover1.jpg]] Open Science and its Discontents  


''edited by'' Gary Hall __TOC__  
[http://www.livingbooksaboutlife.org/books/ISBN_Numbers ISBN: 978-1-60785-267-4]
 
''edited by'' [http://www.livingbooksaboutlife.org/books/Digitize_Me,_Visualize_Me,_Search_Me/bio Gary Hall] __TOC__  


== [http://www.livingbooksaboutlife.org/books/Open_science/Introduction '''Introduction: White Noise: On the Limits of Openness (Living Book Mix)''']  ==
== [http://www.livingbooksaboutlife.org/books/Open_science/Introduction '''Introduction: White Noise: On the Limits of Openness (Living Book Mix)''']  ==


One of the aims of the Living Books About Life series is to provide a 'bridge' or point of connection, translation, even interrogation and contestation, between the humanities and the sciences. Accordingly, this introduction to ''Digitize Me, Visualize Me, Search Me'', a book in the series on open science, takes as its starting point the so-called ‘computational turn’ to data-intensive scholarship in the humanities.  
One of the aims of the Living Books About Life series is to provide a 'bridge' or point of connection, translation, even interrogation and contestation, between the humanities and the sciences. Accordingly, this introduction to ''Digitize Me, Visualize Me, Search Me'' takes as its starting point the so-called ‘computational turn’ to data-intensive scholarship in the humanities.  


The phrase ‘[http://www.thecomputationalturn.com/ the computational turn]’ has been adopted to refer to the process whereby techniques and methodologies drawn from computer science and related fields – including science visualization, interactive information visualization, image processing, network analysis, statistical data analysis, and the management, manipulation and mining of data – are being increasingly used to produce new ways of approaching and understanding texts in the humanities - what is sometimes thought of as 'the digital humanities'. [http://www.livingbooksaboutlife.org/books/Open_science/Introduction (more...)]  
The phrase ‘[http://www.thecomputationalturn.com/ the computational turn]’ has been adopted to refer to the process whereby techniques and methodologies drawn from computer science and related fields – including science visualization, interactive information visualization, image processing, network analysis, statistical data analysis, and the management, manipulation and mining of data – are being increasingly used to produce new ways of approaching and understanding texts in the humanities - what is sometimes thought of as 'the digital humanities'. [http://www.livingbooksaboutlife.org/books/Open_science/Introduction (more...)]  
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=== It’s An Open (Science), Open (Access), Open (Source), Open (Notebook) World  ===
=== It’s An Open (Science), Open (Access), Open (Source), Open (Notebook) World  ===


[http://usefulchem.wikispaces.com/ Open Notebook Science ]  
;[http://usefulchem.wikispaces.com/ Open Notebook Science ]
 
Patrick O. Brown, Michael B. Eisen, Harold Varmus
 
[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0000036 Why PLoS Became a Publisher]<br>


Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk, and Anita Palepu<br>
;Patrick O. Brown, Michael B. Eisen, Harold Varmus&nbsp;
:[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0000036 Why PLoS Became a Publisher]


[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091592/pdf/OpenMed-02-e1.pdf??tool=pmcentrez Open Science, Open Access and Open Source Software at ''Open Medicine'']  
;Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk, and Anita Palepu&nbsp;
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091592/pdf/OpenMed-02-e1.pdf??tool=pmcentrez Open Science, Open Access and Open Source Software at ''Open Medicine'']


=== Community Science  ===
=== Community Science  ===
Line 27: Line 27:
{{#widget:Vimeo|id=12873908}}  
{{#widget:Vimeo|id=12873908}}  


[http://www.psfk.com/2010/09/biocurious-a-community-lab-for-biotechnology.html BioCurious: A Community Lab for Biotechnology]  
;[http://www.psfk.com/2010/09/biocurious-a-community-lab-for-biotechnology.html BioCurious: A Community Lab for Biotechnology]
 
Richard Stallman
 
[http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0020047 Free Community Science and the Free Development of Science]
 
This Revolution Will Be Digitized’: Online Tools for Open Science


[http://biogang.openwetware.org/ Biogang]  
;Richard Stallman&nbsp;
:[http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0020047 Free Community Science and the Free Development of Science]


Bill Hooker
=== 'This Revolution Will Be Digitized’: Online Tools for Open Science  ===


[http://3quarksdaily.blogs.com/3quarksdaily/2007/01/the_future_of_s.html The Future of Science is Open, Part 3: An Open Science World]  
;[http://biogang.openwetware.org/ Biogang]


Chris Patil and Vivian Siegel
;Bill Hooker&nbsp;
:[http://3quarksdaily.blogs.com/3quarksdaily/2007/01/the_future_of_s.html The Future of Science is Open, Part 3: An Open Science World]


[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675795/ This Revolution Will Be Digitized: Online Tools for Radical Collaboration]  
;Chris Patil and Vivian Siegel&nbsp;
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675795/ This Revolution Will Be Digitized: Online Tools for Radical Collaboration]


=== Open Science Publishing  ===
=== Open Science Publishing  ===


Philip E. Bourne  
;Philip E. Bourne&nbsp;
 
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877727/?tool=pmcentrez#pcbi.1000787-Hey1 What Do I Want from the Publisher of the Future?]
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877727/?tool=pmcentrez#pcbi.1000787-Hey1 What Do I Want from the Publisher of the Future?]  


Cameron Neylon  
;Cameron Neylon&nbsp;
 
:[http://pirsa.org/08090038/ Science in the Open/or/How I Learned to Stop Worrying and Love My Blog]
[http://pirsa.org/08090038/ Science in the Open/or/How I Learned to Stop Worrying and Love My Blog]  


== Open Knowledge  ==
== Open Knowledge  ==


=== Open Access to Knowledge ===
=== Access to Knowledge ===


[http://okfn.org/ Open Knowledge Foundation]  
;[http://okfn.org/ Open Knowledge Foundation]


Gaelle Krikorian and Amy Kapczynski, eds,
;Gaelle Krikorian and Amy Kapczynski, eds&nbsp;
:[http://www.soros.org/initiatives/information/focus/access/articles_publications/publications/age-of-intellectual-property-20101110/age-of-intellectual-property-20101110.pdf ''Access to Knowledge In the Age of Intellectual Property'']


[http://www.soros.org/initiatives/information/focus/access/articles_publications/publications/age-of-intellectual-property-20101110/age-of-intellectual-property-20101110.pdf ''Access to Knowledge In the Age of Intellectual Property'']
=== New Models for Open Sharing and Open Research  ===


=== New Models for Open Sharing and Open Research ===
;Anne H. Margulies&nbsp;
:[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020200 A New Model for Open Sharing]


Anne H. Margulies[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020200]  
;Thomas B. Kepler, Marc A. Marti-Renom, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, Matthew H. Todd&nbsp;
:[http://www.publish.csiro.au/nid/51/paper/CH06095.htm Open Source Research - The Power of Us]


[http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020200 A New Model for Open Sharing]
=== Open Knowledge and its Discontents  ===


Thomas B. Kepler, Marc A. Marti-Renom, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, Matthew H. Todd
;J.J. King&nbsp;
:[http://www.metamute.org/proudtobeflesh The Packet Gang: Openness and its Discontents]


[http://www.publish.csiro.au/nid/51/paper/CH06095.htm Open Source Research - The Power of Us]
;Michael Gurstein&nbsp;
 
:[http://gurstein.wordpress.com/2011/07/03/are-the-open-data-warriors-fighting-for-robin-hood-or-the-sheriff-some-reflections-on-okcon-2011-and-the-emerging-data-divide/ Are the Open Data Warriors Fighting for Robin Hood or the Sheriff?: Some Reflections on OKCon 2011 and the Emerging Data Divide]
=== Open Knowledge and its Discontent ===
 
J.J. King
 
[http://www.metamute.org/proudtobeflesh The Packet Gang: Openness and its Discontents]
 
Michael Gurstein  
 
[http://gurstein.wordpress.com/2011/07/03/are-the-open-data-warriors-fighting-for-robin-hood-or-the-sheriff-some-reflections-on-okcon-2011-and-the-emerging-data-divide/ Are the Open Data Warriors Fighting for Robin Hood or the Sheriff?: Some Reflections on OKCon 2011 and the Emerging Data Divide]  


== Open Data  ==
== Open Data  ==


=== Data-Intensive Science ===
=== Data-Intensive Science ===


Vincent S. Smith  
;Vincent S. Smith&nbsp;
:[http://www.biomedcentral.com/1756-0500/2/113 Data Publication: Towards a Database of Everything]


[http://www.biomedcentral.com/1756-0500/2/113 Data Publication: Towards a Database of Everything]  
;Tony Hey, Stewart Tansley, Kristen Tolle, eds&nbsp;
:[http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part4_complete.pdf Scholarly Communication, ''The Fourth Paradigm: Data-Intensive Scientific Discovery'']


Tony Hey, Stewart Tansley, Kristen Tolle, eds
=== World of Data  ===


[http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part4_complete.pdf Scholarly Communication, ''The Fourth Paradigm: Data-Intensive Scientific Discovery'']  
;[http://www.freeourdata.org.uk/ Free Our Data]


World of Data  
;Simon Rogers&nbsp;
:[http://www.guardian.co.uk/news/datablog/2010/nov/09/canada-open-data How Canada Became an Open Data and Data Journalism Powerhouse]


[http://www.freeourdata.org.uk/ Free Our Data]
=== We Can Know It For You  ===


Simon Rogers
;Omer Tene&nbsp;
:[http://epubs.utah.edu/index.php/ulr/article/viewArticle/136 What Google Knows: Privacy and Internet Search Engines]


[http://www.guardian.co.uk/news/datablog/2010/nov/09/canada-open-data How Canada Became an Open Data and Data Journalism Powerhouse]<br>
;Daniel Chandramohan, Kenji Shibuya, Philip Setel, Sandy Cairncross, Alan D. Lopez, Christopher J. L. Murray, Basia Żaba, Robert W. Snow, Fred Binka&nbsp;
 
:[http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0050057 Should Data from Demographic Surveillance Systems Be Made More Widely Available to Researchers?]
=== We Can Know It For You ===
 
Omer Tene
 
[http://epubs.utah.edu/index.php/ulr/article/viewArticle/136 What Google Knows: Privacy and Internet Search Engines]
 
Daniel Chandramohan, Kenji Shibuya, Philip Setel, Sandy Cairncross, Alan D. Lopez, Christopher J. L. Murray, Basia Żaba, Robert W. Snow, Fred Binka  
 
[http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.0050057 Should Data from Demographic Surveillance Systems Be Made More Widely Available to Researchers?]  


== '''Digitize Me'''  ==
== '''Digitize Me'''  ==


=== Encode Me/Decode Me ===
=== Encode Me/Decode Me ===


[http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml Human Genome Project]  
;[http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml Human Genome Project]


The ENCODE Project Consortium  
;The ENCODE Project Consortium&nbsp;
:[http://pubmedcentralcanada.ca/picrender.cgi?accid=PMC3079585&blobtype=pdf&tool=pmcentrez A User's Guide to the Encyclopaedia of DNA Elements (ENCODE) ]


[http://pubmedcentralcanada.ca/picrender.cgi?accid=PMC3079585&blobtype=pdf&tool=pmcentrez A User's Guide to the Encyclopaedia of DNA Elements (ENCODE) ]  
;[http://www.decodeme.com/about-decodeme deCODEme]


[http://www.decodeme.com/about-decodeme deCODEme]
=== Life-Tracking ===
 
=== Life-Tracking ===


{{#widget:Vimeo|id=27381297}}  
{{#widget:Vimeo|id=27381297}}  


[http://quantifiedself.com Quantified Self]  
;[http://quantifiedself.com Quantified Self]


Gary Wolf  
;Gary Wolf&nbsp;
:[http://xrl.us/bh3d4g The Data-Driven Life]


[http://xrl.us/bh3d4g The Data-Driven Life]  
;Aiden R. Doherty and Alan F. Smeaton&nbsp;
:[http://doras.dcu.ie/15300/1/Sensors-03-154-Doherty-ie-edited.pdf Automatically Augmenting Lifelog Events Using Pervasively Generated Content from Millions of People]


Aiden R. Doherty and Alan F. Smeaton
;Jennifer S. Beaudin, Stephen S. Intille, and Margaret E. Morris&nbsp;
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794006/?tool=pmcentrez#ref1 To Track or Not to Track: User Reactions to Concepts in Longitudinal Health Monitoring]


[http://doras.dcu.ie/15300/1/Sensors-03-154-Doherty-ie-edited.pdf Automatically Augmenting Lifelog Events Using Pervasively Generated Content from Millions of People]
=== The Neurological Turn: or, ‘How the Internet Gets Inside Us'  ===


Jennifer S. Beaudin, Stephen S. Intille, and Margaret E. Morris
<youtube>NhLnoZFCDBM</youtube>


[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794006/?tool=pmcentrez#ref1 To Track or Not to Track: User Reactions to Concepts in Longitudinal Health Monitoring]
<br>


<br>
;Adam Gopnik&nbsp;
:[http://www.newyorker.com/arts/critics/atlarge/2011/02/14/110214crat_atlarge_gopnik The Information: How the Internet Gets Inside Us]


=== The Neurological Turn: or, ‘How the Internet Gets Inside Us' ===
;N. Katherine Hayles&nbsp;
:[http://www.sciy.org/2010/11/24/hyper-and-deep-attention-the-generational-divide-in-cognitive-modes-by-n-katherine-hayles/ Hyper and Deep Attention: The Generation Divide in Cognitive Modes]


<youtube>NhLnoZFCDBM</youtube>
;Anna Munster&nbsp;
:[http://computationalculture.net/article/nerves-of-data Nerves of Data: The Neuological Turn In/Against Networked Media]


Adam Gopnik
== '''Visualize Me'''  ==


[http://www.newyorker.com/arts/critics/atlarge/2011/02/14/110214crat_atlarge_gopnik The Information: How the Internet Gets Inside Us]
=== What is Visualization?  ===


N. Katherine Hayles
;Lev Manovich&nbsp;
:[http://manovich.net/blog/wp-content/uploads/2010/10/manovich_visualization_2010.doc What is Visualization?]


[http://www.sciy.org/2010/11/24/hyper-and-deep-attention-the-generational-divide-in-cognitive-modes-by-n-katherine-hayles/ Hyper and Deep Attention: The Generation Divide in Cognitive Modes]  
;Nathan Yau&nbsp;
:[http://flowingdata.com/2011/02/23/data-visualization-meets-game-design-to-explore-your-digital-life/ Data Visualization Meets Game Design to Explore your Digital Life]


== '''Visualize Me'''  ==
;[http://bloom.io/ Bloom]


=== What is Visualization? ===
{{#widget:Vimeo|id=8569187}}


Lev Manovich
;Keiichi Matsuda
:[http://www.keiichimatsuda.com/augmented.php Augmented (hyper)Reality: Domestic Robocop]


[http://manovich.net/blog/wp-content/uploads/2010/10/manovich_visualization_2010.doc What is Visualization?]
=== Mood-mapping  ===


Nathan Yau
;Celeste Biever&nbsp;
:[http://www.newscientist.com/article/dn19200-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter Mood Maps Reveal Emotional States of America]


[http://flowingdata.com/2011/02/23/data-visualization-meets-game-design-to-explore-your-digital-life/ Data Visualization Meets Game Design to Explore your Digital Life]  
;[http://www.newscientist.com/articlevideo/dn19200/221111468001-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter mood video]


[http://bloom.io/ Bloom]  
<youtube>ZglPWYb8X2o</youtube> [http://www.moodscope.com/]  


=== Mood-mapping ===
;[http://www.moodscope.com/ Moodscope]


Celeste Biever
;[http://www.mappiness.org.uk Mappiness]


[http://www.newscientist.com/article/dn19200-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter Mood Maps Reveal Emotional States of America]
=== The Visualized Human (or, The Human As Spectacle)  ===


[http://www.newscientist.com/articlevideo/dn19200/221111468001-twitter-mood-maps-reveal-emotional-states-of-america.html Twitter mood video] <youtube>ZglPWYb8X2o</youtube> [http://www.moodscope.com/ Moodscope]  
;Nicholas Felton&nbsp;
:[http://feltron.com/ The Annual Felton Report]


[http://www.mappiness.org.uk Mappiness]
<youtube>RE4ce4mexrU</youtube>


=== The Visualized Human ===
;Deb Roy&nbsp;
:[http://www.youtube.com/watch?v=RE4ce4mexrU&feature=youtu.be The Birth of a Word]


Nicholas Felton
;Johanna Drucker&nbsp;
:[http://mit.tv/y7OwFq Humanistic Approaches to the Graphical Expression of Interpretation]


[http://feltron.com/ The Annual Felton Report] <youtube>RE4ce4mexrU</youtube> Deb Roy
== Search Me  ==


[http://www.youtube.com/watch?v=RE4ce4mexrU&feature=youtu.be The Birth of a Word] {{#widget:Drucker Video}} Johanna Drucker
=== Search-Engine Science  ===


[http://mitworld.mit.edu/video/796 Humanistic Approaches to the Graphical Expression of Interpretation]  
;Emily H. Chan, Vikram Sahai, Corrie Conrad, and John S. Brownstein&nbsp;
:[http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC3104029&tool=pmcentrez Using Web Search Query Data to Monitor Dengue Epidemics: A New Model for Neglected Tropical Disease Surveillance]


== Search Me  ==
;Annie Y.S. Lau, Enrico Coiera, Tatjana Zrimec, and Paul Compton&nbsp;
:[http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC2956236&tool=pmcentrez Clinician Search Behaviors May Be Influenced by Search Engine Design]


=== Search-Engine Science ===
:[https://brandyourself.com/ BrandYourself]


Emily H. Chan, Vikram Sahai, Corrie Conrad, and John S. Brownstein
=== The Science of Control  ===


[http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC3104029&tool=pmcentrez Using Web Search Query Data to Monitor Dengue Epidemics: A New Model for Neglected Tropical Disease Surveillance]  
;Alession Signorini, Alberto Maria Segre, Philip M. Polgreen&nbsp;
:[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019467 The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. During the Influenza A H1N1 Pandemic]


Annie Y.S. Lau, Enrico Coiera, Tatjana Zrimec, and Paul Compton
;David Parry&nbsp;
:[http://www.livingbooksaboutlife.org/books/Surveillance ''Surveillance'' ]


[http://pubmedcentralcanada.ca/articlerender.cgi?accid=PMC2956236&tool=pmcentrez Clinician Search Behaviors May Be Influenced by Search Engine Design]  
;Felix Stalder and Christine Mayer&nbsp;
:[http://felix.openflows.com/node/113 The Second Index: Search Engines, Personalization and Surveillance (Deep Search)]


=== The Science of Control ===
=== Deep Search  ===


Alession Signorini Alberto Maria Segre, Philip M. Polgreen
{{#widget:Vimeo|id=13456992}}


[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019467 The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. During the Influenza A H1N1 Pandemic]  
;Michael K. Bergman&nbsp;
:[http://quod.lib.umich.edu/cgi/t/text/text-idx?c=jep;view=text;rgn=main;idno=3336451.0007.104 The Deep Web: Surfacing Hidden Value]


David Parry
;Clare Birchall&nbsp;
:[http://www.livingbooksaboutlife.org/books/The_in/visible The Invisible Web, ''The In/Visible'']


[http://www.livingbooksaboutlife.org/books/Surveillance ''Surveillance'' ]
== Media Gifts?  ==


Felix Stalder and Christine Mayer
{{#widget:Vimeo|id=8223187}} [http://www.suicidemachine.org/]


[http://felix.openflows.com/node/113 The Second Index: Search Engines, Personalization and Surveillance (Deep Search)]  
;[http://www.suicidemachine.org/ Web 2.0 Suicide Machine]


=== Deep Search ===
;[http://transparencygrenade.com/ Transparency Grenade]


{{#widget:Vimeo|id=13456992}} Michael K. Bergman
;[http://www.freedomboxfoundation.org/ Freedom Box Foundation]


[http://quod.lib.umich.edu/cgi/t/text/text-idx?c=jep;view=text;rgn=main;idno=3336451.0007.104 The Deep Web: Surfacing Hidden Value]  
;[http://yacy.net/en/index.html/ YaCy]


Clare Birchall
;[http://navasse.net/traceblog/about.html Traceblog]


[http://www.livingbooksaboutlife.org/books/The_in/visible The Invisible Web, ''The In/Visible'']  
;[http://turbulence.org/Works/JJPS/extension The JJPS Firefox Extension]


== Media Gifts? ==
;[http://www.weavrs.com/find/ Weavers]


{{#widget:Vimeo|id=8223187}} [http://www.suicidemachine.org/ Web 2.0 Suicide Machine]  
;[http://bengrosser.com/projects/facebook-demetricator/ Facebook Demetricator]


[http://www.freedomboxfoundation.org/ Freedom Box Foundation]  
;[http://prisom.me/ #PRISOM]


[http://navasse.net/traceblog/about.html Traceblog]  
;[http://givememydata.com/ Give Me My Data]


[http://turbulence.org/Works/JJPS/extension The JJPS Firefox Extension]  
;[http://commodify.us/ commodify.us]


== Appendix  ==
== Appendix  ==
Line 243: Line 247:
<youtube>ukNkx45Ua0Y</youtube>  
<youtube>ukNkx45Ua0Y</youtube>  


Karl Popper, The Open Society and its Enemies  
;Karl Popper, The Open Society and its Enemies
 
== [http://www.livingbooksaboutlife.org/books/Open_science/Attributions Attributions]  ==
 
== A 'Frozen' PDF Version of this Living Book  ==


[http://www.livingbooksaboutlife.org/books/Open_science/Attributions Attributions]
;[http://livingbooksaboutlife.org/pdfs/bookarchive/DigitizeMe.pdf Download a 'frozen' PDF version of this book as it appeared on 7th October 2011]

Latest revision as of 08:57, 12 November 2013

LifetrackingCover1.jpg
LifetrackingCover1.jpg

Open Science and its Discontents

ISBN: 978-1-60785-267-4

edited by Gary Hall

Introduction: White Noise: On the Limits of Openness (Living Book Mix)

One of the aims of the Living Books About Life series is to provide a 'bridge' or point of connection, translation, even interrogation and contestation, between the humanities and the sciences. Accordingly, this introduction to Digitize Me, Visualize Me, Search Me takes as its starting point the so-called ‘computational turn’ to data-intensive scholarship in the humanities.

The phrase ‘the computational turn’ has been adopted to refer to the process whereby techniques and methodologies drawn from computer science and related fields – including science visualization, interactive information visualization, image processing, network analysis, statistical data analysis, and the management, manipulation and mining of data – are being increasingly used to produce new ways of approaching and understanding texts in the humanities - what is sometimes thought of as 'the digital humanities'. (more...)

Open Science

It’s An Open (Science), Open (Access), Open (Source), Open (Notebook) World

Open Notebook Science
Patrick O. Brown, Michael B. Eisen, Harold Varmus 
Why PLoS Became a Publisher
Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk, and Anita Palepu 
Open Science, Open Access and Open Source Software at Open Medicine

Community Science

BioCurious: A Community Lab for Biotechnology
Richard Stallman 
Free Community Science and the Free Development of Science

'This Revolution Will Be Digitized’: Online Tools for Open Science

Biogang
Bill Hooker 
The Future of Science is Open, Part 3: An Open Science World
Chris Patil and Vivian Siegel 
This Revolution Will Be Digitized: Online Tools for Radical Collaboration

Open Science Publishing

Philip E. Bourne 
What Do I Want from the Publisher of the Future?
Cameron Neylon 
Science in the Open/or/How I Learned to Stop Worrying and Love My Blog

Open Knowledge

Access to Knowledge

Open Knowledge Foundation
Gaelle Krikorian and Amy Kapczynski, eds 
Access to Knowledge In the Age of Intellectual Property

New Models for Open Sharing and Open Research

Anne H. Margulies 
A New Model for Open Sharing
Thomas B. Kepler, Marc A. Marti-Renom, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, Matthew H. Todd 
Open Source Research - The Power of Us

Open Knowledge and its Discontents

J.J. King 
The Packet Gang: Openness and its Discontents
Michael Gurstein 
Are the Open Data Warriors Fighting for Robin Hood or the Sheriff?: Some Reflections on OKCon 2011 and the Emerging Data Divide

Open Data

Data-Intensive Science

Vincent S. Smith 
Data Publication: Towards a Database of Everything
Tony Hey, Stewart Tansley, Kristen Tolle, eds 
Scholarly Communication, The Fourth Paradigm: Data-Intensive Scientific Discovery

World of Data

Free Our Data
Simon Rogers 
How Canada Became an Open Data and Data Journalism Powerhouse

We Can Know It For You

Omer Tene 
What Google Knows: Privacy and Internet Search Engines
Daniel Chandramohan, Kenji Shibuya, Philip Setel, Sandy Cairncross, Alan D. Lopez, Christopher J. L. Murray, Basia Żaba, Robert W. Snow, Fred Binka 
Should Data from Demographic Surveillance Systems Be Made More Widely Available to Researchers?

Digitize Me

Encode Me/Decode Me

Human Genome Project
The ENCODE Project Consortium 
A User's Guide to the Encyclopaedia of DNA Elements (ENCODE)
deCODEme

Life-Tracking

Quantified Self
Gary Wolf 
The Data-Driven Life
Aiden R. Doherty and Alan F. Smeaton 
Automatically Augmenting Lifelog Events Using Pervasively Generated Content from Millions of People
Jennifer S. Beaudin, Stephen S. Intille, and Margaret E. Morris 
To Track or Not to Track: User Reactions to Concepts in Longitudinal Health Monitoring

The Neurological Turn: or, ‘How the Internet Gets Inside Us'


Adam Gopnik 
The Information: How the Internet Gets Inside Us
N. Katherine Hayles 
Hyper and Deep Attention: The Generation Divide in Cognitive Modes
Anna Munster 
Nerves of Data: The Neuological Turn In/Against Networked Media

Visualize Me

What is Visualization?

Lev Manovich 
What is Visualization?
Nathan Yau 
Data Visualization Meets Game Design to Explore your Digital Life
Bloom

Keiichi Matsuda
Augmented (hyper)Reality: Domestic Robocop

Mood-mapping

Celeste Biever 
Twitter Mood Maps Reveal Emotional States of America
Twitter mood video

[1]

Moodscope
Mappiness

The Visualized Human (or, The Human As Spectacle)

Nicholas Felton 
The Annual Felton Report

Deb Roy 
The Birth of a Word
Johanna Drucker 
Humanistic Approaches to the Graphical Expression of Interpretation

Search Me

Search-Engine Science

Emily H. Chan, Vikram Sahai, Corrie Conrad, and John S. Brownstein 
Using Web Search Query Data to Monitor Dengue Epidemics: A New Model for Neglected Tropical Disease Surveillance
Annie Y.S. Lau, Enrico Coiera, Tatjana Zrimec, and Paul Compton 
Clinician Search Behaviors May Be Influenced by Search Engine Design
BrandYourself

The Science of Control

Alession Signorini, Alberto Maria Segre, Philip M. Polgreen 
The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. During the Influenza A H1N1 Pandemic
David Parry 
Surveillance
Felix Stalder and Christine Mayer 
The Second Index: Search Engines, Personalization and Surveillance (Deep Search)

Deep Search

Michael K. Bergman 
The Deep Web: Surfacing Hidden Value
Clare Birchall 
The Invisible Web, The In/Visible

Media Gifts?

[2]

Web 2.0 Suicide Machine
Transparency Grenade
Freedom Box Foundation
YaCy
Traceblog
The JJPS Firefox Extension
Weavers
Facebook Demetricator
#PRISOM
Give Me My Data
commodify.us

Appendix

Karl Popper, The Open Society and its Enemies

Attributions

A 'Frozen' PDF Version of this Living Book

Download a 'frozen' PDF version of this book as it appeared on 7th October 2011
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